First, let me say that I am enjoying this discussion. Lately, not many interesting questions are being submitted.
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With regard to an a SEP Form 5330, Return of Excise Taxes Related to Employee Benefit Plans, is used to report the 10 percent excise tax on the following:
• Nondeductible employer contributions to SEPs, [IRC 4972(d)(1)(A)(ii)]
• Prohibited transactions [IRC 4975(a), 4975(e)(1)]
• Excess contributions to plans with cash or deferred arrangements [IRC 4979(a), 4979(e)(4)]
etc etc
refer
http://www.irs.ustreas.gov/cgi/websys_fmanage - the form and
http://ftp.fedworld.gov/pub/irs-pdf/i5330.pdf - the instructions
It seems to me than that none of these apply to this situation, therefore, the form is not necessary.
The problem is the employer did not follow the written contribution formula according to the plan he/she adopted, therefore, what we have here is a SEP allocation excess (Prop. Treas. Reg. Sec. 1.408-7(f))
If the allocation formula, according to the SEP document is not followed, the SEP could be disqualified, especially if it is determined that contributions were made in favor of highly compensated employees.
One way of correcting such excess is to make contributions for those employees who received insufficient contributions, however, as I stated before ,this correction must be made before the employers tax return due date plus extensions.
The other option is to revise the compensation of the employee/s who received the excess contribution Prop. Treas. Reg. 1.408-7(f). See This reg provided a formula for making this correction.
Since the lowest common denominator is "0%;" all contributions are excesses under the regulations. (Moderator)